Python io.BufferedReader() Examples

def read_fastq(filename):
    """
    return a stream of FASTQ entries, handling gzipped and empty files
    """
    if not filename:
        return itertools.cycle((None,))
    if filename == "-":
        filename_fh = sys.stdin
    elif filename.endswith('gz'):
        if is_python3():
            filename_fh = gzip.open(filename, mode='rt')
        else:
            filename_fh = BufferedReader(gzip.open(filename, mode='rt'))
    else:
        filename_fh = open(filename)
    return stream_fastq(filename_fh) 

def get_SHA1(file_value: io.BufferedReader):
    """
    Get SHA1 hash of the file, directly in memory
    TODO : Fix the input type
    :param file_value: A file to compute the SHA-1
    :return: the SHA-1 of the file in memory
    """

    h = hashlib.sha1()
    b = bytearray(128 * 1024)
    mv = memoryview(b)

    for n in iter(lambda: file_value.readinto(mv), 0):
        h.update(mv[:n])

    return h.hexdigest() 

def __init__(self, course_file: BufferedReader = None, dryrun=False, debug=False, helm_args=None, continue_on_error=False, create_namespace=True):
        self.config = Config()
        self.results = ReckonerInstallResults()
        self.config.dryrun = dryrun
        self.config.debug = debug
        self.config.helm_args = helm_args
        self.config.continue_on_error = continue_on_error
        self.config.create_namespace = create_namespace
        if course_file:
            self.config.course_path = course_file.name

        if self.config.debug:
            logging.warn("The --debug flag will be deprecated.  Please use --helm-args or --dry-run instead.")
        if self.config.helm_args:
            logging.warn("Specifying --helm-args on the cli will override helm_args in the course file.")

        self.course = Course(course_file) 

def test_invalid_schema_resource(self, tmpdir, caplog, schema):
        class FakeProvider(object):
            def get_resource_stream(self, pkg, rsc):
                return io.BufferedReader(io.BytesIO(schema))

        # pkg_resources.resource_stream() cannot be mocked directly
        # Instead mock the module-level function it calls.
        (flexmock(pkg_resources)
            .should_receive('get_provider')
            .and_return(FakeProvider()))

        filename = os.path.join(str(tmpdir), 'config.yaml')
        with open(filename, 'w'):
            pass

        tasker, workflow = self.prepare()
        plugin = ReactorConfigPlugin(tasker, workflow, config_path=str(tmpdir))
        with caplog.at_level(logging.ERROR), pytest.raises(Exception):
            plugin.run()

        captured_errs = [x.message for x in caplog.records]
        assert any("cannot validate" in x for x in captured_errs) 

def from_fileobj(cls, fileobj, byteorder="big"):
        """Load an nbt file from a proper file object.

        The method is used by the :func:`load` helper function when the
        ``gzipped`` keyword-only argument is not specified explicitly.

        Arguments:
            fileobj:
                Can be either a standard ``io.BufferedReader`` for
                uncompressed nbt or a ``gzip.GzipFile`` for gzipped nbt
                data. The function simply calls the inherited
                :meth:`nbtlib.tag.Compound.parse` classmethod and sets the
                :attr:`filename` and :attr:`gzipped` attributes depending
                on the argument.

            byteorder:
                Can be either ``"big"`` or ``"little"``. The argument is
                forwarded to :meth:`nbtlib.tag.Compound.parse`.
        """
        self = cls.parse(fileobj, byteorder)
        self.filename = getattr(fileobj, "name", self.filename)
        self.gzipped = isinstance(fileobj, gzip.GzipFile)
        self.byteorder = byteorder
        return self 

def test_fetch_files_function(tmpdir):
    # Setup and run three experiments
    root = tmpdir.strpath
    run_test_experiment(exp_name="experiment 1 alpha", exp_id="1234", root_dir=root)
    run_test_experiment(exp_name="experiment 2 beta", exp_id="5678", root_dir=root)
    run_test_experiment(
        exp_name="experiment 3 alpha beta", exp_id="9990", root_dir=root
    )

    tinydb_reader = TinyDbReader(root)

    res = tinydb_reader.fetch_files(indices=0)
    assert len(res) == 1
    assert list(res[0]["artifacts"].keys()) == ["about"]
    assert isinstance(res[0]["artifacts"]["about"], io.BufferedReader)
    assert res[0]["date"] == datetime.datetime(1999, 5, 4, 3, 2, 1)
    assert res[0]["exp_id"] == "1234"
    assert res[0]["exp_name"] == "experiment 1 alpha"
    assert list(res[0]["resources"].keys()) == ["sacred/__init__.py"]
    assert isinstance(res[0]["resources"]["sacred/__init__.py"], io.BufferedReader)
    assert list(res[0]["sources"].keys()) == ["setup.py"]
    assert isinstance(res[0]["sources"]["setup.py"], io.BufferedReader) 

def _body_file__get(self):
        """
            Input stream of the request (wsgi.input).
            Setting this property resets the content_length and seekable flag
            (unlike setting req.body_file_raw).
        """
        if not self.is_body_readable:
            return io.BytesIO()
        r = self.body_file_raw
        clen = self.content_length
        if not self.is_body_seekable and clen is not None:
            # we need to wrap input in LimitedLengthFile
            # but we have to cache the instance as well
            # otherwise this would stop working
            # (.remaining counter would reset between calls):
            #   req.body_file.read(100)
            #   req.body_file.read(100)
            env = self.environ
            wrapped, raw = env.get('webob._body_file', (0,0))
            if raw is not r:
                wrapped = LimitedLengthFile(r, clen)
                wrapped = io.BufferedReader(wrapped)
                env['webob._body_file'] = wrapped, r
            r = wrapped
        return r 

def idzip_compression(path, output):
        '''Compress a file using  idzip, a gzip-compatible format with random access support.
        '''
        if output is None:
            output = '-'
        with click.open_file(output, mode='wb') as outfh:
            writer = _compression.GzipFile(fileobj=outfh, mode='wb')
            with click.open_file(path, 'rb') as infh:
                try:
                    infh_wrap = io.BufferedReader(infh)
                    header = infh_wrap.peek(2)
                    if _compression.starts_with_gz_magic(header):
                        click.echo("Detected gzip input file", err=True)
                        infh_wrap = _compression.GzipFile(fileobj=infh_wrap)
                except AttributeError:
                    infh_wrap = infh
                buffer_size = _compression.WRITE_BUFFER_SIZE
                chunk = infh_wrap.read(buffer_size)
                while chunk:
                    writer.write(chunk)
                    chunk = infh_wrap.read(buffer_size)
            writer.close() 

def backport_makefile(self, mode="r", buffering=None, encoding=None,
                      errors=None, newline=None):
    """
    Backport of ``socket.makefile`` from Python 3.5.
    """
    if not set(mode) <= {"r", "w", "b"}:
        raise ValueError(
            "invalid mode %r (only r, w, b allowed)" % (mode,)
        )
    writing = "w" in mode
    reading = "r" in mode or not writing
    assert reading or writing
    binary = "b" in mode
    rawmode = ""
    if reading:
        rawmode += "r"
    if writing:
        rawmode += "w"
    raw = SocketIO(self, rawmode)
    self._makefile_refs += 1
    if buffering is None:
        buffering = -1
    if buffering < 0:
        buffering = io.DEFAULT_BUFFER_SIZE
    if buffering == 0:
        if not binary:
            raise ValueError("unbuffered streams must be binary")
        return raw
    if reading and writing:
        buffer = io.BufferedRWPair(raw, raw, buffering)
    elif reading:
        buffer = io.BufferedReader(raw, buffering)
    else:
        assert writing
        buffer = io.BufferedWriter(raw, buffering)
    if binary:
        return buffer
    text = io.TextIOWrapper(buffer, encoding, errors, newline)
    text.mode = mode
    return text 

def isfileobj(f):
        return isinstance(f, (io.FileIO, io.BufferedReader)) 

def test_file_as_input(tmp_path):
    f = tmp_path / "hello.txt"
    f.write_text("123")

    input_args = ["-l", "python", str(f)]
    args = cli.parse_args(input_args)

    assert args.language == "python"

    assert isinstance(args.infile, io.BufferedReader)
    assert args.infile.name == str(f) 

def backport_makefile(self, mode="r", buffering=None, encoding=None,
                      errors=None, newline=None):
    """
    Backport of ``socket.makefile`` from Python 3.5.
    """
    if not set(mode) <= {"r", "w", "b"}:
        raise ValueError(
            "invalid mode %r (only r, w, b allowed)" % (mode,)
        )
    writing = "w" in mode
    reading = "r" in mode or not writing
    assert reading or writing
    binary = "b" in mode
    rawmode = ""
    if reading:
        rawmode += "r"
    if writing:
        rawmode += "w"
    raw = SocketIO(self, rawmode)
    self._makefile_refs += 1
    if buffering is None:
        buffering = -1
    if buffering < 0:
        buffering = io.DEFAULT_BUFFER_SIZE
    if buffering == 0:
        if not binary:
            raise ValueError("unbuffered streams must be binary")
        return raw
    if reading and writing:
        buffer = io.BufferedRWPair(raw, raw, buffering)
    elif reading:
        buffer = io.BufferedReader(raw, buffering)
    else:
        assert writing
        buffer = io.BufferedWriter(raw, buffering)
    if binary:
        return buffer
    text = io.TextIOWrapper(buffer, encoding, errors, newline)
    text.mode = mode
    return text 

def backport_makefile(self, mode="r", buffering=None, encoding=None,
                      errors=None, newline=None):
    """
    Backport of ``socket.makefile`` from Python 3.5.
    """
    if not set(mode) <= {"r", "w", "b"}:
        raise ValueError(
            "invalid mode %r (only r, w, b allowed)" % (mode,)
        )
    writing = "w" in mode
    reading = "r" in mode or not writing
    assert reading or writing
    binary = "b" in mode
    rawmode = ""
    if reading:
        rawmode += "r"
    if writing:
        rawmode += "w"
    raw = SocketIO(self, rawmode)
    self._makefile_refs += 1
    if buffering is None:
        buffering = -1
    if buffering < 0:
        buffering = io.DEFAULT_BUFFER_SIZE
    if buffering == 0:
        if not binary:
            raise ValueError("unbuffered streams must be binary")
        return raw
    if reading and writing:
        buffer = io.BufferedRWPair(raw, raw, buffering)
    elif reading:
        buffer = io.BufferedReader(raw, buffering)
    else:
        assert writing
        buffer = io.BufferedWriter(raw, buffering)
    if binary:
        return buffer
    text = io.TextIOWrapper(buffer, encoding, errors, newline)
    text.mode = mode
    return text 

def backport_makefile(self, mode="r", buffering=None, encoding=None,
                      errors=None, newline=None):
    """
    Backport of ``socket.makefile`` from Python 3.5.
    """
    if not set(mode) <= {"r", "w", "b"}:
        raise ValueError(
            "invalid mode %r (only r, w, b allowed)" % (mode,)
        )
    writing = "w" in mode
    reading = "r" in mode or not writing
    assert reading or writing
    binary = "b" in mode
    rawmode = ""
    if reading:
        rawmode += "r"
    if writing:
        rawmode += "w"
    raw = SocketIO(self, rawmode)
    self._makefile_refs += 1
    if buffering is None:
        buffering = -1
    if buffering < 0:
        buffering = io.DEFAULT_BUFFER_SIZE
    if buffering == 0:
        if not binary:
            raise ValueError("unbuffered streams must be binary")
        return raw
    if reading and writing:
        buffer = io.BufferedRWPair(raw, raw, buffering)
    elif reading:
        buffer = io.BufferedReader(raw, buffering)
    else:
        assert writing
        buffer = io.BufferedWriter(raw, buffering)
    if binary:
        return buffer
    text = io.TextIOWrapper(buffer, encoding, errors, newline)
    text.mode = mode
    return text 

def isfileobj(f):
        return isinstance(f, (io.FileIO, io.BufferedReader, io.BufferedWriter)) 

def backport_makefile(self, mode="r", buffering=None, encoding=None,
                      errors=None, newline=None):
    """
    Backport of ``socket.makefile`` from Python 3.5.
    """
    if not set(mode) <= {"r", "w", "b"}:
        raise ValueError(
            "invalid mode %r (only r, w, b allowed)" % (mode,)
        )
    writing = "w" in mode
    reading = "r" in mode or not writing
    assert reading or writing
    binary = "b" in mode
    rawmode = ""
    if reading:
        rawmode += "r"
    if writing:
        rawmode += "w"
    raw = SocketIO(self, rawmode)
    self._makefile_refs += 1
    if buffering is None:
        buffering = -1
    if buffering < 0:
        buffering = io.DEFAULT_BUFFER_SIZE
    if buffering == 0:
        if not binary:
            raise ValueError("unbuffered streams must be binary")
        return raw
    if reading and writing:
        buffer = io.BufferedRWPair(raw, raw, buffering)
    elif reading:
        buffer = io.BufferedReader(raw, buffering)
    else:
        assert writing
        buffer = io.BufferedWriter(raw, buffering)
    if binary:
        return buffer
    text = io.TextIOWrapper(buffer, encoding, errors, newline)
    text.mode = mode
    return text 

def _makefile(sock, mode):
        return io.BufferedReader(SocketIO(sock, mode)) 

def test_buffered_reader(self):
        # Issue #7471: a GzipFile can be wrapped in a BufferedReader for
        # performance.
        self.test_write()

        with gzip.GzipFile(self.filename, 'rb') as f:
            with io.BufferedReader(f) as r:
                lines = [line for line in r]

        self.assertEqual(lines, 50 * data1.splitlines(True)) 

def _get_text_stdin(buffer_stream):
    text_stream = _NonClosingTextIOWrapper(
        io.BufferedReader(_WindowsConsoleReader(STDIN_HANDLE)),
        'utf-16-le', 'strict', line_buffering=True)
    return ConsoleStream(text_stream, buffer_stream) 

def test_buffered_reader(self):
        # Issue #7471: a GzipFile can be wrapped in a BufferedReader for
        # performance.
        self.test_write()

        with gzip.GzipFile(self.filename, 'rb') as f:
            with io.BufferedReader(f) as r:
                lines = [line for line in r]

        self.assertEqual(lines, 50 * data1.splitlines(True)) 

def _buffered_read_file(fobj):
    """Return a buffered version of a read file object."""
    if PY27 and bz2 is not None and isinstance(fobj, bz2.BZ2File):
        # Python 2.7 doesn't work with BZ2File through a buffer: "no
        # attribute 'readable'" error.
        return fobj
    else:
        return io.BufferedReader(fobj, buffer_size=_IO_BUFFER_SIZE) 

def _makefile(sock, mode):
        return io.BufferedReader(SocketIO(sock, mode)) 

def backport_makefile(self, mode="r", buffering=None, encoding=None,
                      errors=None, newline=None):
    """
    Backport of ``socket.makefile`` from Python 3.5.
    """
    if not set(mode) <= set(["r", "w", "b"]):
        raise ValueError(
            "invalid mode %r (only r, w, b allowed)" % (mode,)
        )
    writing = "w" in mode
    reading = "r" in mode or not writing
    assert reading or writing
    binary = "b" in mode
    rawmode = ""
    if reading:
        rawmode += "r"
    if writing:
        rawmode += "w"
    raw = SocketIO(self, rawmode)
    self._makefile_refs += 1
    if buffering is None:
        buffering = -1
    if buffering < 0:
        buffering = io.DEFAULT_BUFFER_SIZE
    if buffering == 0:
        if not binary:
            raise ValueError("unbuffered streams must be binary")
        return raw
    if reading and writing:
        buffer = io.BufferedRWPair(raw, raw, buffering)
    elif reading:
        buffer = io.BufferedReader(raw, buffering)
    else:
        assert writing
        buffer = io.BufferedWriter(raw, buffering)
    if binary:
        return buffer
    text = io.TextIOWrapper(buffer, encoding, errors, newline)
    text.mode = mode
    return text 

def backport_makefile(self, mode="r", buffering=None, encoding=None,
                      errors=None, newline=None):
    """
    Backport of ``socket.makefile`` from Python 3.5.
    """
    if not set(mode) <= set(["r", "w", "b"]):
        raise ValueError(
            "invalid mode %r (only r, w, b allowed)" % (mode,)
        )
    writing = "w" in mode
    reading = "r" in mode or not writing
    assert reading or writing
    binary = "b" in mode
    rawmode = ""
    if reading:
        rawmode += "r"
    if writing:
        rawmode += "w"
    raw = SocketIO(self, rawmode)
    self._makefile_refs += 1
    if buffering is None:
        buffering = -1
    if buffering < 0:
        buffering = io.DEFAULT_BUFFER_SIZE
    if buffering == 0:
        if not binary:
            raise ValueError("unbuffered streams must be binary")
        return raw
    if reading and writing:
        buffer = io.BufferedRWPair(raw, raw, buffering)
    elif reading:
        buffer = io.BufferedReader(raw, buffering)
    else:
        assert writing
        buffer = io.BufferedWriter(raw, buffering)
    if binary:
        return buffer
    text = io.TextIOWrapper(buffer, encoding, errors, newline)
    text.mode = mode
    return text 

def readable(self):
    # io.BufferedReader needs us to appear readable
    return True 

def isfileobj(f):
        return isinstance(f, (io.FileIO, io.BufferedReader, io.BufferedWriter)) 

def backport_makefile(self, mode="r", buffering=None, encoding=None,
                      errors=None, newline=None):
    """
    Backport of ``socket.makefile`` from Python 3.5.
    """
    if not set(mode) <= set(["r", "w", "b"]):
        raise ValueError(
            "invalid mode %r (only r, w, b allowed)" % (mode,)
        )
    writing = "w" in mode
    reading = "r" in mode or not writing
    assert reading or writing
    binary = "b" in mode
    rawmode = ""
    if reading:
        rawmode += "r"
    if writing:
        rawmode += "w"
    raw = SocketIO(self, rawmode)
    self._makefile_refs += 1
    if buffering is None:
        buffering = -1
    if buffering < 0:
        buffering = io.DEFAULT_BUFFER_SIZE
    if buffering == 0:
        if not binary:
            raise ValueError("unbuffered streams must be binary")
        return raw
    if reading and writing:
        buffer = io.BufferedRWPair(raw, raw, buffering)
    elif reading:
        buffer = io.BufferedReader(raw, buffering)
    else:
        assert writing
        buffer = io.BufferedWriter(raw, buffering)
    if binary:
        return buffer
    text = io.TextIOWrapper(buffer, encoding, errors, newline)
    text.mode = mode
    return text 

def test_happy_path(self):
        url = 'https://example.com/path/file'
        dest_dir = tempfile.mkdtemp()
        content = b'abc'
        reader = BufferedReader(BytesIO(content), buffer_size=1)
        responses.add(responses.GET, url, body=reader)
        result = download_url(url, dest_dir)

        assert os.path.basename(result) == 'file'
        with open(result, 'rb') as f:
            assert f.read() == content 

def backport_makefile(self, mode="r", buffering=None, encoding=None,
                      errors=None, newline=None):
    """
    Backport of ``socket.makefile`` from Python 3.5.
    """
    if not set(mode) <= set(["r", "w", "b"]):
        raise ValueError(
            "invalid mode %r (only r, w, b allowed)" % (mode,)
        )
    writing = "w" in mode
    reading = "r" in mode or not writing
    assert reading or writing
    binary = "b" in mode
    rawmode = ""
    if reading:
        rawmode += "r"
    if writing:
        rawmode += "w"
    raw = SocketIO(self, rawmode)
    self._makefile_refs += 1
    if buffering is None:
        buffering = -1
    if buffering < 0:
        buffering = io.DEFAULT_BUFFER_SIZE
    if buffering == 0:
        if not binary:
            raise ValueError("unbuffered streams must be binary")
        return raw
    if reading and writing:
        buffer = io.BufferedRWPair(raw, raw, buffering)
    elif reading:
        buffer = io.BufferedReader(raw, buffering)
    else:
        assert writing
        buffer = io.BufferedWriter(raw, buffering)
    if binary:
        return buffer
    text = io.TextIOWrapper(buffer, encoding, errors, newline)
    text.mode = mode
    return text 

def backport_makefile(self, mode="r", buffering=None, encoding=None,
                      errors=None, newline=None):
    """
    Backport of ``socket.makefile`` from Python 3.5.
    """
    if not set(mode) <= set(["r", "w", "b"]):
        raise ValueError(
            "invalid mode %r (only r, w, b allowed)" % (mode,)
        )
    writing = "w" in mode
    reading = "r" in mode or not writing
    assert reading or writing
    binary = "b" in mode
    rawmode = ""
    if reading:
        rawmode += "r"
    if writing:
        rawmode += "w"
    raw = SocketIO(self, rawmode)
    self._makefile_refs += 1
    if buffering is None:
        buffering = -1
    if buffering < 0:
        buffering = io.DEFAULT_BUFFER_SIZE
    if buffering == 0:
        if not binary:
            raise ValueError("unbuffered streams must be binary")
        return raw
    if reading and writing:
        buffer = io.BufferedRWPair(raw, raw, buffering)
    elif reading:
        buffer = io.BufferedReader(raw, buffering)
    else:
        assert writing
        buffer = io.BufferedWriter(raw, buffering)
    if binary:
        return buffer
    text = io.TextIOWrapper(buffer, encoding, errors, newline)
    text.mode = mode
    return text